Details of this dataset
Gambia_Indie-MH, 4 plates prepped between 2023_03 & 2023_04
Import data
Sample size, loci BEFORE cleanup
Explore data structure
## [1] "Sample size = 346"
## [1] "Loci = 244"
## [1] "1 to 130 alleles per locus per sample"
Merging data (TBD)
Combine multiple sequencing runs
Combine read coverage with parasite density
Adding plate map
Negative controls
Do neg ctrls have a lot of reads?
Positive controls
Using a known parasite strain at a known density
Alleles should be known, and monoclonal
## [1] "Mean of total locus = 214, Mean prop. of monoclonal loci = 0.85, Mean prop. of polyclonal loci = 0.15"
Look at total amplification
All pools combined
##
## 1A 1AB 1B 1B2 2
## 165 5 75 2 29
Species check
Should be Pfal, and not other species
These loci will be filtered out downstream (loci 1AB)
Look at how each individual pool amplified
Pool 1A
## [1] "No reads in any samples for these loci, for 1A"
## # A tibble: 0 × 3
## # ℹ 3 variables: locus <chr>, pool <chr>, n <dbl>
## [1] "List of samples that do not have >75% loci with >100 reads, in pool 1A"
## # A tibble: 172 × 7
## # Groups: sampleID [172]
## sampleID pool totreads n50 n100 neg_control norm
## <chr> <chr> <int> <int> <int> <lgl> <dbl>
## 1 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 235 0 0 FALSE 0
## 2 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 1989 4 0 FALSE 0
## 3 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 8057 61 18 FALSE 0.112
## 4 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 464 0 0 FALSE 0
## 5 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 989 0 0 FALSE 0
## 6 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 2786 7 0 FALSE 0
## 7 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 4984 28 6 FALSE 0.0375
## 8 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 7523 63 16 FALSE 0.1
## 9 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 9277 77 23 FALSE 0.144
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1A 698 0 0 FALSE 0
## # ℹ 162 more rows
Pool 5
##
## TRUE
## 47
## [1] "Loci without any reads, pool 5"
## # A tibble: 0 × 16
## # ℹ 16 variables: locus-pool <chr>, Category <chr>, chr_malaria <chr>,
## # ampInsert_start <dbl>, ampInsert_end <dbl>, GeneID <chr>, Gene <chr>,
## # Reason_to_include_(if_drug_resistance:_aminoacids) <chr>,
## # Amino_acid_range_(*:_partial_coverage_of_that_aminoacid) <chr>,
## # pool5 <lgl>, amplicon_id <chr>, amplicon_start <dbl>, amplicon_end <dbl>,
## # fwd_primer <chr>, rev_primer <chr>, n <dbl>
## [1] "List of samples that do not have >75% alleles with >100 reads, pool 5"
## # A tibble: 154 × 7
## # Groups: sampleID [154]
## sampleID pool totreads n50 n100 neg_control norm
## <chr> <chr> <int> <int> <int> <lgl> <dbl>
## 1 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 86 0 0 FALSE 0
## 2 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 647 2 0 FALSE 0
## 3 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 3216 22 10 FALSE 0.227
## 4 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 138 0 0 FALSE 0
## 5 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 364 0 0 FALSE 0
## 6 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 862 2 0 FALSE 0
## 7 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 1550 14 3 FALSE 0.0682
## 8 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 2037 18 5 FALSE 0.114
## 9 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 3295 24 15 FALSE 0.341
## 10 Gambia_Indie-1B_MH_1_AE_2023_0… 1B 266 0 0 FALSE 0
## # ℹ 144 more rows
Pool 2
## Rows: 31 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (10): locus-pool, Category, chr_malaria, GeneID, Gene, Reason to include...
## dbl (4): ampInsert_start, ampInsert_end, amplicon_start, amplicon_end
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Create list of samples that fail any of the QC checks by pool
Reprep if <50% amplicons with >100 reads
Repool if >50% but <75% amplicons with >100 reads
##
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185300_PR1A5_S298
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185323_PR1A5_S218
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185326_PR1A5_S242
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185343_PR1A5_S264
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185391_PR1A5_S214
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185401_PR1A5_S216
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185567_PR1A5_S229
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185722_PR1A5_S250
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185876_PR1A5_S288
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185891_PR1A5_S276
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185903_PR1A5_S262
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068185939_PR1A5_S274
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186025_PR1A5_S286
## 1
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186063_PR1A5_S300
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186076_PR1A5_S287
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186110_PR1A5_S240
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186138_PR1A5_S263
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068186207_PR1A5_S241
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279974_PR1A5_S306
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279988_PR1A5_S293
## 1
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279991_PR1A5_S304
## 1
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068279996_PR1A5_S255
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280016_PR1A5_S283
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280025_PR1A5_S284
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280046_PR1A5_S261
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280050_PR1A5_S224
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280052_PR1A5_S248
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280058_PR1A5_S303
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280081_PR1A5_S268
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280088_PR1A5_S285
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280106_PR1A5_S221
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280181_PR1A5_S295
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280188_PR1A5_S249
## 1
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280201_PR1A5_S256
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280279_PR1A5_S222
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280282_PR1A5_S236
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280290_PR1A5_S257
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280303_PR1A5_S246
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280304_PR1A5_S282
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280374_PR1A5_S266
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280398_PR1A5_S272
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280432_PR1A5_S260
## 2
## Gambia_Indie-1B_MH_1_AE_2023_03_06_8068280471_PR1A5_S225
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279954_PR1A5_S391
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279957_PR1A5_S370
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279962_PR1A5_S369
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279967_PR1A5_S380
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279976_PR1A5_S356
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279983_PR1A5_S335
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279990_PR1A5_S314
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068279999_PR1A5_S403
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280004_PR1A5_S316
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280029_PR1A5_S317
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280043_PR1A5_S333
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280059_PR1A5_S321
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280060_PR1A5_S373
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280071_PR1A5_S358
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280080_PR1A5_S357
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280095_PR1A5_S332
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280117_PR1A5_S319
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280118_PR1A5_S382
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280144_PR1A5_S381
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280165_PR1A5_S343
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280195_PR1A5_S334
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280206_PR1A5_S350
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280213_PR1A5_S325
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280215_PR1A5_S384
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280218_PR1A5_S328
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280219_PR1A5_S383
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280224_PR1A5_S389
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280236_PR1A5_S312
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280243_PR1A5_S346
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280250_PR1A5_S401
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280252_PR1A5_S385
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280286_PR1A5_S344
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280296_PR1A5_S387
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280300_PR1A5_S348
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280312_PR1A5_S378
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280323_PR1A5_S386
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280325_PR1A5_S364
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280326_PR1A5_S400
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280411_PR1A5_S371
## 1
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280421_PR1A5_S374
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280430_PR1A5_S322
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280506_PR1A5_S399
## 2
## Gambia_Indie-1B_MH_2_AE_2023_03_28_8068280520_PR1A5_S331
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279968_PR1A5_S449
## 1
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279985_PR1A5_S441
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068279995_PR1A5_S429
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280003_PR1A5_S423
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280006_PR1A5_S434
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280007_PR1A5_S448
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280020_PR1A5_S499
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280045_PR1A5_S463
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280048_PR1A5_S442
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280074_PR1A5_S457
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280083_PR1A5_S415
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280090_PR1A5_S409
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280101_PR1A5_S446
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280104_PR1A5_S484
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280116_PR1A5_S435
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280124_PR1A5_S420
## 1
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280151_PR1A5_S493
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280159_PR1A5_S440
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280162_PR1A5_S410
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280164_PR1A5_S436
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280177_PR1A5_S462
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280184_PR1A5_S491
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280196_PR1A5_S458
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280203_PR1A5_S445
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280207_PR1A5_S468
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280231_PR1A5_S470
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280235_PR1A5_S424
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280239_PR1A5_S406
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280276_PR1A5_S492
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280283_PR1A5_S454
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280288_PR1A5_S456
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280298_PR1A5_S482
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280310_PR1A5_S426
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280315_PR1A5_S466
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280316_PR1A5_S479
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280320_PR1A5_S464
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280334_PR1A5_S467
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280346_PR1A5_S485
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280349_PR1A5_S407
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280351_PR1A5_S425
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280375_PR1A5_S418
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280393_PR1A5_S495
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280394_PR1A5_S431
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280396_PR1A5_S408
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280406_PR1A5_S497
## 1
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280409_PR1A5_S472
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280414_PR1A5_S432
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280429_PR1A5_S413
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280460_PR1A5_S444
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280469_PR1A5_S428
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280481_PR1A5_S476
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280485_PR1A5_S412
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280505_PR1A5_S447
## 2
## Gambia_Indie-1B_MH_3_AE_2023_03_30_8068280683_PR1A5_S477
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279948_PR1A5_S518
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279953_PR1A5_S516
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279965_PR1A5_S545
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279981_PR1A5_S558
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068279993_PR1A5_S550
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280023_PR1A5_S551
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280027_PR1A5_S534
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280057_PR1A5_S541
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280126_PR1A5_S503
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280130_PR1A5_S528
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280134_PR1A5_S539
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280160_PR1A5_S519
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280211_PR1A5_S513
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280220_PR1A5_S530
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280225_PR1A5_S535
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280227_PR1A5_S557
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280237_PR1A5_S560
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280244_PR1A5_S548
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280292_PR1A5_S559
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280416_PR1A5_S537
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280419_PR1A5_S549
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280427_PR1A5_S556
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280440_PR1A5_S561
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280511_PR1A5_S538
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280512_PR1A5_S544
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280632_PR1A5_S527
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280637_PR1A5_S529
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280659_PR1A5_S536
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280666_PR1A5_S555
## 1
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280680_PR1A5_S552
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280685_PR1A5_S526
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280697_PR1A5_S531
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280711_PR1A5_S508
## 2
## Gambia_Indie-1B_MH_4_AE_2023_04_05_8068280715_PR1A5_S543
## 2
## Joining with `by = join_by(sampleID)`
Filtering
Remove bad samples
Remove bad loci
Remove controls
## [1] "Sample size= 151"
## [1] "# of entries excluded = 0, Prop. excluded = 0"
## [1] "# of loci after cleanup = 242"
## character(0)
